The present thesis focuses on the elucidation of human mitochondrial inner membrane presequence-translocation machinery with implications on cancer cell proliferation. Mitochondria are the endosymbiotic organelles in an eukaryotic cell performing a vast repertoire of functions and require approximately 1500 proteins. However, the mitochondria genome contains only 13 protein-coding genes primarily transcribing the complexes of the electron transport chain. Therefore, it is evident that most of the mitochondrial proteome is encoded by the nucleus and synthesized on cytosolic ribosomes. Chapter 1: Mechanism of mitochondrial inner membrane protein translocation and its oncogenic connection. Mitochondria consist of different routes of directing proteins to their intramitochondrial destinations. The presequence pathway, mediated by the inner membrane TIM23 complex, is responsible for the import of matrix and a number of single transmembrane helixes containing inner membrane proteins. This pathway accounts for approximately 60% of the total proteome imported into the organelle and hence, is the major focus of discussion in the present study. The components of the TIM23 complex can be subdivided into two groups, the protein conducting channel and the import motor. The initial translocation across the TIM23 channel utilizes the electrochemical membrane potential that exists across the inner membrane whereas the final step of the translocation process is driven by energy from ATP hydrolysis. MtHsp70 forms the central component of the import motor, and its function is regulated by the J-proteins. Pam18 stimulates the ATPase activity of mtHsp70. Pam16, on the other hand, forms a subcomplex with Pam18 and exerts an inhibitory effect its ATPase stimulatory activity, in turn regulating the activity of the import motor. The stoichiometric coupling with the substrate binding-release cycle of mtHsp70 drives the import process. Although the organization of presequence translocation machinery and its functional annotations have been described in detail in yeast system, little information is available on its organization in human. It is difficult to contemplate the existence of similar machinery in human mitochondria with complex and diversified functions. Human mitochondria apart from regulating the metabolic pathways are involved in progression of cancer, neurodegenerative disorders, responses to xenobiotic stress and induction of apoptosis. Numerous reports have shown that mutations and overexpression of human orthologs of translocase components are associated with various cancer subtypes. Such disease condition also involves targeting of specific cell signaling molecules that reprogram organellar functions and alter the cellular phenotype. Based on this evidence we defined our study into four broad objectives – 1) identify the components of human presequence translocase as Chapter two and three, 2) characterize the subunit organization of human presequence translocation machinery in Chapter four, 3) determine the functional connection between the translocase components and the cancer phenotype in Chapter four and five and 4) understand how the functions of J-proteins have evolved across the species as Chapter six. Chapter 2: Unraveling the role of Magmas in human mitochondrial protein transport. Pam16 plays a critical role in regulation of import process by governing the activity of the import motor. Proteins orthologous to Pam16 had been reported earlier to be overexpressed in various metabolically active tissues and cancer subtypes. We found that in humans a protein named as Mitochondria Associated Granulocyte Macrophage colony Stimulating factor signaling molecule (Magmas) showed significant sequence similarity with yeast Pam16 at its C-terminal region. Magmas was initially discovered as a protein that was overexpressed in neoplastic prostrate and when the cells were exposed to GM-CSF. Our experiments suggested that Magmas localized in human and yeast mitochondria and it was associated with the inner mitochondrial membrane. Magmas could complement the growth of yeast cells that were deleted for the essential gene PAM16 and could import precursor proteins into the mitochondria. Like Pam16, Magmas was able to form a stable heterodimeric subcomplex with yeast Pam18 and human Pam18 ortholog DnaJC19 (JC19). We found that J-domain forms the minimal region required for heterodimer formation between Magmas and Pam18/JC19. Mutations in Magmas J-like domain resulted in temperature sensitive growth phenotypes in yeast cells and associated import defect in translocating precursor proteins into the organelle due to inability to form a stable subcomplex with Pam18 and JC19, resulting in loss of import function. Loss of subcomplex formation leads to dissociation of Pam18 from the translocation machinery highlighting the importance of Magmas in tethering Pam18/JC19 to the presequence translocase. Magmas, showing characteristic of a J-like protein, was unable to stimulate the ATPase activity of mtHsp70. However, it exerted an inhibitory effect on the ATP stimulatory effect of the J-protein Pam18/JC19, indicating that Magmas has a regulatory effect on the overall activity of import motor. In contrast Magmas mutants those are incapable of forming a stable heterodimer with Pam18 were unable to regulate the activity of Pam18 resulting in import defects. In summary, our results highlight that Magmas is an ortholog of yeast Pam16 performing similar functions at the import channel. Chapter 3: Existence of two J-protein subcomplexes at the translocation channel with distinct physiological functions. JC19 has been regarded as the human ortholog of Pam18 whose loss of function was associated with dilated cardiomyopathy and ataxia syndrome. However, immunoprecipitation analysis using anti-Magmas antibody revealed the presence of a second J-protein identified as DnaJC15 (JC15) that shared a highly similar J-domain with JC19. JC15 was initially identified as a protein whose loss in expression resulted in development of a chemoresistant phenotype in ovarian carcinoma cells exposed to chemotherapeutic treatment. We found that JC15 localizes in mitochondria where it was associated with the inner membrane. Similar to Pam18 and JC19, JC15 heterodimerized with Magmas/Pam16 through its J-domain and associated with the presequence translocase of the inner membrane. A loss of function mutation at the J-domain of JC15 destabilizes its interaction with Magmas resulting in protein translocation defects and temperature-sensitive growth phenotype in yeast cells. The JC15 mutant showed inability to get associated with the translocation channel and had dysregulated stimulation of mtHsp70 activity leading to decreased mitochondria biogenesis and loss of mitochondrial membrane potential. In summary, our results showed that JC15 is the second human ortholog of Pam18 with similar functions. In contrast to yeast, in human mitochondria JC15 and JC19 were found to form two separate and distinct J-protein subcomplexes with Magmas at the mitochondrial import motor. The essentiality of the J-proteins for normal human mitochondria function was addressed through siRNA mediated downregulation of Magmas, JC19 and JC15. We found that Magmas and JC19 are essential for normal mitochondrial function and cell viability whereas JC15 is dispensable and might have a supportive role. Interestingly, both JC19 and JC15 interacted with Magmas with equal affinity and stimulated mtHsp70’s ATPase activity by equivalent levels. This shows that both JC19 and JC15 share similar properties in terms of their functions at the import channel, and the differences might be in a much broader perspective in terms of their association with the translocation channel. Chapter 4: Architecture of human mitochondrial inner membrane presequence -translocation machinery. In yeast, there exists a single J-protein subcomplex formed by Pam16 and Pam18, which is recruited to the sole translocase. However, humans present a completely different scenario where there exists a two distinct subcomplexes formed by Magmas with either of the J-proteins. So the question arises how the individual subcomplexes is recruited to the translocation machinery; whether they are associated to one or differentially recruited to two different translocases. We identified the existence of three distinct translocases in the human system constituted by the two J-proteins along with the Tim17 paralogs. JC15 along with Tim17a forms the translocase A of size similar to that of the yeast system, and it forms the ancestral translocase in the humans. Tim17b isoforms, on the other hand, associates with JC19 to form mammalian specific translocases B1 and B2. The association of the J-proteins at the translocation channel was found to be mediated by Magmas as a subcomplex. Downregulation of Magmas resulted in dissociation of both the J-proteins, and its overexpression resulted in redistribution of J-proteins at the translocases. We found that translocase B imported precursor proteins at a comparatively higher rate as compared to translocase A. Disruption of translocase B had deleterious effects on cell viability, respiratory chain complex's activities, Fe-S cluster biogenesis, mitochondria morphology, regulation of free radical levels and maintenance of mitochondrial genome. In contrast, depletion of translocase A did not significantly alter the survivability of cells, mitochondrial activity and maintenance of organellar morphology. This shows that translocase B is essential and performs the constitutive import function in the mammalian system whereas translocase A is dispensable and might have a supportive role in maintenance of mitochondrial function. However, translocase A play a specific role in human mitochondria in context to cancer cells. We observed that the elevated level of Tim17a found in cancer cells is responsible for maintenance of higher mitochondrial DNA copy number and higher proliferative potential of cancer cells. Additionally, translocase A also plays a specific role in translocation of cell signaling proteins that lack a mitochondrial targeting sequence into the mitochondria, highlighting the possible role of this translocase in neoplastic transformation. Chapter 5: Mechanistic insights into the role of JC15 as a part of translocase A in chemoresistant phenotype. JC15 had been initially identified to be associated with development of chemoresistance in cancer cells. However, the molecular mechanism followed by the protein has not been elucidated yet. Our studies have shown that overexpression of JC15 leads to increased sensitivity of cells to chemotherapeutic drug cisplatin and are coupled with complete loss of membrane potential, mitochondrial swelling and cytochrome c release. However, this chemosensitive phenotype was partially ameliorated upon preexposing the cell to cyclosporine A which is an inhibitor of cyclophilin D, a critical component of mitochondrial membrane transition pore (MPTP) complex. A similar reversal of phenotype was observed upon depleting cyclophilin D even under JC15 overexpressing background. This highlighted a possible functional connection between these two proteins. In order to check this hypothesis other way around, we overexpressed cyclophilin D in the cells which resulted in constitutive opening of the MPTP complex, enhanced mitochondrial swelling and reduced cell viability. In contrast, the gain of function anomalies of cyclophilin D overexpression was significantly reversed upon JC15 depletion. We observed through co-immunoprecipitation analysis that JC15 activates cyclophilin D by releasing it from the inhibitory effects of TRAP1 and couples it to the MPTP complex. Additionally, we have also shown that the J-domain of JC15 is critical for its interaction with cyclophilin D and loss of function mutation at the J-domain of JC15 disrupts its interaction with cyclophilin D. As a result the JC15 mutant is not able to mount a chemosensitive response to cisplatin drug. Chapter 6: Identification of regions determining the divergence of J-proteins functions at the mitochondrial import motor. The above studies show ample evidence to suggest that the two human J-proteins have undergone significant divergence in their function in human mitochondria in spite of having a highly similar J-domain. Therefore, we asked the question that how the human J-proteins have evolved and diversified from the primitive yeast protein Pam18 and what are the regional determinants in the protein sequence that dictate the function of the J-domain. We utilized a purely genetic approach to address the problem. We observed that JC19 was unable to rescue the growth of yeast cells deleted for the essential gene Pam18 and JC15 expression resulted in cold sensitive phenotype. We used JC15 as the model protein for our assays and applied three methodologies. First, generation and isolation of a series of mutations in JC15 that could rescue the cold sensitive phenotype, and the growth of the cells were similar to the wild type. Second, to identify the regulatory residues by isolation of second site suppressors that could be the suppressor the mutant phenotypes isolated earlier. Third, we utilized a purely evolutionary approach by swapping the individual domains between the three J-proteins- Pam18, JC19 and JC15. Our genetic data support the idea that the partial loss of function of human J-protein in the yeast system is due to altered subcomplex dynamics with Pam16. The altered dynamics of the subcomplex is mainly regulated by the residues in the arm, linker and helical regions of the J-domain, especially the helix II regions. Our analysis has also uncovered a critical role of the targeting (T) region of J-proteins which along with inter-membrane space (IMS) domain share significant sequence diversity among J-proteins in yeast and humans. The T-region in conjunction with the IMS domain plays a crucial role in regulating the J-domain’s function across the kingdoms and within the species. Although, our genetic data needs to be supplemented with biochemical evidence, this study provides significant insights into the diversity of J-protein function across the species and mode of their regulation through regions flanking the J-domain.

The Twin arginine translocation pathway translocates fully folded proteins across cellular membranes and is only utilised by proteins that fold before translocation. It is a unique process that is found in many bacteria, archaea and also in plant chloroplasts. Investigation of the bacterial and thylakoidal systems has revealed much of the substrates and the components involved in their translocation. Unfortunately, there are still many unanswered questions such as how substrates are directed to the membrane and the actual mechanism of translocation. This thesis specifically investigates the Tat pathway of halophilic and thermophilic archaea. To date, there has been a lack of research into the archaeal Tat pathway and it is possible that there are unique adaptations because of the extreme environments that these organisms inhabit. Chapter 3 specifically investigates the thermophiles Sulfolobus solfataricus and Sulfolobus tokodaii and attempts to purify their Tat complexes. By doing so it was hoped to learn more about the Tat components and their interactions. Further experiments were also performed to determine if the two S. solfataricus Tat operons provide specificity to the Tat substrates that translocate. Four separate areas of the Tat pathway of halophilic archaea (haloarchaea) were investigated in Chapters 4-7. Firstly, site-directed mutagenesis was used to analyse the signal peptides of haloarchaeal Tat substrates in more detail. Consequently, the resulting data led to the use of bioinformatics to analyse the Haloarchaeal signal peptide. The bioenergetics of the Tat system was then determined by analysing the effect of a variety of ionophores on translocation of the Tat substrates AmyH and SptA. Finally, a series of folding and stability assays were used to increase our understanding of AmyH, which could provide further information on why this protein, like many other haloarchaeal proteins, requires the Tat pathway for translocation.

During the synthesis of secretory and membrane proteins, polypeptides move through a universally conserved protein-conducting channel, formed by the Sec61/SecY complex that is located in the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. The channel operates in two different modes depending on its binding partners. In co-translational translocation, a pathway found in all organisms, the channel associates with a translating ribosome. In post-translational translocation, the channel cooperates with either the Sec62–Sec63 complex in eukaryotes or the SecA ATPase in bacteria. Despite tremendous progress in our understanding of protein translocation over the past decades, many questions about its mechanism remain to be answered. These include (1) how the channel maintains the membrane barrier for small molecules while transporting large proteins, (2) what is the functional implication of channel oligomerization, and (3) how the channel interacts with binding partners and polypeptide substrates during translocation. To address these questions, we developed a novel in vivo method to generate both co- and post-translation translocation intermediates in intact Escherichia coli cells, such that polypeptide chains are only partially translocated through the channel. Using this method, we first demonstrated that a translocating polypeptide itself blocks small molecules from passing through an open SecY channel. A hydrophobic pore ring surrounding the polypeptide chain is vital for maintaining the membrane barrier during translocation. Next, we examined the importance of SecY oligomerization in protein translocation. Crosslinking experiments showed that SecY molecules interact with each other in native membranes, but that this self-association is greatly decreased upon insertion of polypeptide substrates. We also showed that SecY mutants that cannot form oligomers are still functional in vivo. Collectively, our data indicate that a single copy of SecY is sufficient for protein translocation. Finally, we isolated an intact co-translational translocation intermediate from E. coli cells and analyzed its structure by cryo-electron microscopy. An initial map shows a translating ribosome containing all three tRNAs is bound to one copy of the SecY channel. Analysis of a large dataset is ongoing in order to understand the structural basis of how the channel interacts with the ribosome and translocating nascent chain.

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No description available.

Im Rahmen dieser Arbeit wurde die Konservierung elektrophysiologischer Charakteristika von Proteintranslokasen aus verschiedenen Organismen untersucht. Die Sec61/Sec61p Komplexe aus rauen Mikrosomen von Canis familiaris und Saccharomyces cerevisiae bilden ionenpermeable Poren mit einer hohen Leitfähigkeit in planaren Lipidmembranen. In Säugerzellen werden diese durch einen Calcium-Calmodulin (Ca2+-CaM)-vermittelten negativen Feedback-Mechanismus reguliert. Im Rahmen dieser Arbeit konnte die Spezifität der zugrundeliegenden Interaktion von Ca2+-CaM mit der α-Untereinheit des Sec61 Komplexes belegt werden. Es wurde gezeigt, dass der Calmodulin Antagonist Ophiobolin A in der Lage ist, die Inhibition der Ionenpermeation durch Sec61 aufzuheben. Des Weiteren wurde anhand elektrophysiologischer Messungen nachgewiesen, dass dieser Ca2+-CaM-vermittelte Regulationsmechanismus in der Hefe S. cerevisiae nicht vorhanden ist. Dies wird auf eine kritische Variation in der Primärstruktur des Hefe-Proteins zurückgeführt, welche die Bindung von Calmodulin an den N-Terminus von Sec61p verhindert. Der bakterielle SecYEG Komplex aus E. coli konnte erfolgreich in Proteoliposomen rekonstituiert werden. Die Funktionalität des Translokons wurde in in vitro proOmpA Importexperimenten nachgewiesen. Mittels dieser Proteoliposomen sollten SecYEG Poren in den planaren Bilayer integriert werden. Sowohl für den inaktiven als auch für den durch die Anwesenheit von Substraten oder Bindepartnern aktivierten Komplex konnten keine ionenpermeablen Poren in der Membran nachgewiesen werden. Dies lässt darauf schließen, dass im Gegensatz zu den homologen Komplexen in Eukaryoten, der bakterielle Sec Komplex intrinsisch die Permeabilitätsbarriere für Ionen aufrechterhält. Die vorliegenden Ergebnisse legen nahe, dass weder die Ausbildung ionenpermeabler Poren, noch deren Regulation zwischen den Sec Komplexen von Bakterien, Hefen und Säugern vollständig konserviert ist. In einem zweiten Teilprojekt wurden auf der Suche nach der zentralen Proteinimportpore in der äußeren Mitochondrienmembran von Trypanosoma brucei zwei mögliche Kandidaten, TbSam50 und ATOM, anhand elektrophysiologischer Untersuchungen verglichen. Beide waren in der Lage in planaren Bilayern ionenpermeable Poren auszubilden. Die elektrophysiologischen Grundcharakteristika dieser Poren, wie der hohe Leitwert und die Selektivität für Kationen sowie die beobachtete Interaktion mit mitochondrialen Präsequenzen, stimmen gut mit einer potentiellen Funktion als Proteinimportpore überein. Eine detaillierte Untersuchung der Einzelkanaleigenschaften zeigte, dass TbSam50 beträcht-liche Ähnlichkeiten zu homologen Proteinen in Hefen und menschlichen Zellen aufweist. Somit bestätigen die hier präsentierten Ergebnisse die Identifikation von TbSam50 als Kern der trypanosomalen Assemblierungsmaschinerie für β-barrel Proteine in der äußeren Mitochondrienmembran. Besonderheiten in der Beeinflussung der Kanaleigenschaften durch mitochondriale Präpeptide, insbesondere die erhöhte Verweildauer des Kanals im geschlossenen Zustand, weisen darauf hin, dass TbSam50 keine duale Funktion als β-barrel Insertase und Proteintranslokase besitzt. Hingegen lieferte die elektrophysiologische Charakterisierung von ATOM Hinweise, welche die Identifikation dieses Proteins als porenbildende Untereinheit des mitochondrialen Proteinimportapparates in T. brucei bestätigen. Darüber hinaus zeigten Vergleiche der elektrophysiologischen Charakteristika, insbesondere des Schaltverhaltens und der Anzahl porenbildender Untereinheiten pro aktiver Einheit im artifiziellen Bilayer, dass ATOM stärkere Ähnlichkeiten zu Proteintranslokasen bakterieller Abstammung aufweist, als zu Tom40, der generellen Importpore der Eukaryoten. Dies unterstützt das auf Sequenzvergleichen basierende Model, dass ATOM ein evolutives Relikt repräsentiert, anhand dessen die Entwicklung der mitochondrialen Proteinimportmaschinerie aus einer bakteriellen, Omp85-artigen Protein-exportpore abgeleitet werden kann.

No description available.

Membrane compartmentalisation allows eukaryotic cells to perform complex processes by combining dedicated sets of proteins in the same organelle. To achieve this, the cell must first target the appropriate proteins, primarily synthesised on cytosolic ribosomes, to the correct subcellular location. Components of the secretory pathway/endomembrane system begin this journey via their signal sequence-dependent delivery to the endoplasmic reticulum (ER). These ER targeting signals are hydrophobic, and typically function whilst the protein is being synthesised, via a so-called 'co-translational' pathway. However, some hydrophobic signals can also facilitate post-translational protein targeting to the ER, or initiate regulated protein degradation in the cytosol. Tail-anchored (TA) proteins are transmembrane proteins with a single C-terminal transmembrane domain that functions as both their subcellular targeting signal and membrane anchor. Recent evidence suggests that the canonical TRC40 pathway, through which mammalian TA proteins are delivered to the ER, may not be essential in vivo. In this thesis, I provide functional evidence for the existence of an orthologous SRP-independent (SND) pathway in mammalian cells and identify roles for both the signal recognition particle (SRP)-mediated pathway and presumptive mammalian SND pathway in the biogenesis of TA proteins. I conclude that although TRC40 normally plays a role in TA protein biogenesis, it is not essential, and speculate that these alternative pathways make a significant contribution to the apparent redundancy of the TRC40 pathway in vivo. The soluble components that act upstream of TRC40 during protein biogenesis also play an important role in the recognition and selective degradation of hydrophobic membrane and secretory proteins that mislocalise to the cytosol. I now provide preliminary evidence that TRC40 appears to exhibit dual functionality, having a non-essential role in TA protein delivery, whilst also contributing to protein quality control by acting as a putative holdase. My data suggest that both TRC40 and BAG6 can influence the proteasomal degradation of a novel class of substrates, which I have termed the aberrant short secretory proteins.

E. coli SecA is an essential component for protein translocaiton across membrane. SecA can be deleted from its N- and/or C-terminal ends without losing complementation activity. In this study, we determined the dispensity of both ends of SecA molecule. The minimal length at the SecA C-terminus is dependent on the length of the N-terminal region. SecA10-826 and SecA22-829 are the two minimal length SecAs. One more amino acid deleted at the C-terminal end completely abolished their complementation activity. A hydrophobic amino acid is required at the 826th amino acid in the minimal-length SecAs. Both SecA22-828 and SecA22-829 could form a dimer, and have decreased ATPase and protein translocation activities. The active truncated SecA mutants tended to have more soluble form than membrane-bound form, but were stably embedded in membrane. In contrast, the inactive truncated SecA mutants tended to have more membrane-bound form, but were not stable in membrane. Thus, the loss of complementation is not related to dimerization, ATPase and translocation activity but to certain extent related to their biased subcelluar localization and conformation in membrane. Isolated membranes of E coli strains were solubilized and fractionated by sucrose gradient fractionation. These membranes fractions were depleted of SecY and YidC, but contained SecD, SecF and GroEL. Proteoliposomes reconstituted from these fractionated membrane proteins were active in pOmpA translocation which required SecA and ATP. Membrane fractions from strain CK1801 in which the unc gene is deleted were reconstituted into liposomes and also showed translocation activities. Moreover, proteoliposomes reconstituted with Bacteriorodopsin alone were not active in translocation, while proteoliposomes reconstituted with Bacteriorodopsin and CK1801 membrane fractions showed elevated translocation efficiency. These data suggested that proton motive force is not obligatory for, but stimulatory to translocation of pOmA. Purified GroEL was reconstituted into lipsomes and the reconstituted proteoliposomes were active in pOmpA translocation although at lower efficiency. This translocation also required SecA and ATP. These results together suggested that translocation of pOmpA is active in the absence of SecY and YidC. In the absence of SecYEG, translocation of pOmpA requires SecA and ATP. GroEL, SecD and SecF may participate in the SecY-independent translocation.

Protein translocation is essential for bacterial survival and the most important translocation mechanism in bacteria is the secretion (Sec) pathway. Thus targeting Sec pathway is a promising strategy for developing novel antibacterial therapeutics. We report the design, syntheses, mechanistic studies and structure-activity relationship studies using HQSAR and 3-D QSAR Topomer CoMFA analyses of 4-oxo-5-cyano thiouracil derivatives. In summary, introduction of polar group such as –N3 and linker groups such as –CH2-O- enhanced the potency as well as logP and logS several fold. We also report the discovery, optimization and structure-activity relationship study of 1,2,4-triazole containing pyrimidines as novel, highly potent antimicrobial agents. A number of inhibitors have been found to inhibit microbial growth at high nanomolar concentrations.